Pokemon Alters
by blueeyesdarkmagic
Summary: Mokuba gets trapped in the pokemon world a week later Seto, Yugi, and Joey join him. Read as they fight Team Flare and fufill a prophecy and Mokuba is the main main character. Seto, Yugi, and Joey are his helpers.
1. Welcome to the Pokemon world

**Kaiba's POV**

I am more confused now than when I found out about Priest Seto . I looked around seeing nothing but fog and the unconscious bodies of Yugi and Joey. 'Great.' I though sarcastically . Earlier I was sitting at my desk filling out paperwork. Then there was a bright light, and now I'm here. I heard a moan and saw Yugi and Joey starting to get up. "Where in the name of Ra are we?" asked Joey. " I have no idea." I answered. " I see you are all awake . " said a voice " Show yourself." I demanded**.** " As you wish." It answered. I soon saw a black streak run in front. It looked like a fox and I had no idea what I was looking at.{**a/n: Ok now before you read ahead see if you can guess what pokemon this is same with the others too.} "**Hello I'm Zorua and I am one of the pokemon that have brought you here." "And I'm the second." We all looked over to what I describe as a green hedgehog with flowers. "I'm Shaymin." It said. "And I am Victini." Then we all looked at some beige thing with big ears that formed a V. "Who are you and what are we doing here?" asked Yugi. " We are pokemon and you are here to save Kalos from Team Flare. The legendary trainer has passed and Team Flare has made a comeback." answered Zorua bluntly. "Ok I'm lost." said Joey. To be honest I was too but my pride wouldn't let me admit it." I see we need to give you a rundown on pokemon. " said Shaymin. {**a/n Blah blah I wont do this part blah blah . } **"Ok now you need pokemon so pick two of your duel monsters but it has to be a beast, winged-beast, dragon, or a fiend that looks like a beast. IT CANT HAVE HUMAN CHARACTERISTICS." said Zorua. I saw Yugi pout , I'm guessing he wanted to pick Dark Magician." I pick Blue-eyes and Alexandrite Dragon." I said. Joey picked Red-eyes and Leogun. Yugi picked Kuriboh and Slifer the sky dragon. " Ok give us a minute." said Victini. Another bright light appeared and it soon vanished. "Here are your poke-balls. Now to make sure you now how to use them each of you release a pokemon." ordered Shaymin. I pressed the button and threw mine . Out came a real flesh and blood Blue-eyes. "Now that's a Blue-eyes." I said awe-struck. Joey threw his and out came Red-eyes. "Okay awesome." gaped Joey. Yugi threw his and out came Kuriboh which immediately nuzzled Yugi. Me and Joey were petting our dragons. "Now you must go but we will meet again." said Zorua. And I didn't doubt him. "Remember to look up as much as possible." said Shaymin. "Lie as much as you need to." encouraged Victini. "No problem on that." said Joey. "Don't worry when you finish your mission you will go home. And Kaiba." said Zorua."Yes?""Well your about to hate me but where do you think Mokuba was for the past week." My eyes widened. " So he went where we're going?" "Yep he's been learning about pokemon and since he didn't have a deck we gave him an Eevee."said Victini. "Don't worry he isn't far from your landing spot." smiled Shaymin. "Wait landing sp..." but before I could finish I saw us spiraling towards the ground.

**Normal POV**

Seto immediately brought out Blue-eyes and he landed on it's back. Joey did the same with Red-eyes and Yugi with Slifer. 'Oh my god why are all of our dragons so huge, mainly Slifer. God how are we not attracting attention?' thought Joey. They all landed and thanked their dragons and left for the nearest town, wherever that was. Their first priority, for Kaiba's sake, is to find Mokuba.

a/n : well there is the first chapter hoped you like and Mokuba will have a bigger role than just being missing so yea. also flames are welcome I use them to help me. and one more thing tell me if you would prefer a Yugi vs. Kaiba pokemon battle or a Joey vs. Kaiba pokemon battle then I'll make Mokuba battle the guy left yea r&r


	2. Mokuba vs Grunt

**Blue: Hello guys I'm back. Mokuba is the main character of this chapter.**

**Mokuba: So I'm in the spotlight.**

**Blue: Yep lets just say that in the Pokémon world you have more power than Seto.**

**Seto: But I have a blue-eyes in the flesh.**

**Blue: Yes but do you know its moves.**

**Seto: White Lightning.**

**Blue: That's not a Pokémon move.**

**Seto: Damn it.**

**Mokuba: Blue does not own Pokémon or Yugioh.**

* * *

Mokuba and his Eevee were enjoying lunch. Mokuba had a turkey sandwich while Eevee had Pokémon food sprinkled with Oran Berry powder.

"How is it Eevee?" he asked his little partner. Eevee looked like a small beige fox with a lighter brown tipped tail.

Even though he'd only been here for a week he had grown attached to little fuzzball. He was sweet, cute, lovable, and protective.

He acted like Seto sometimes, and that made Mokuba miss him all the more.

"Eevee." replied the little Pokémon, bobbing its head up and down as if to say good.

Mokuba just smiled. Soon a bright light enveloped the field they were sitting in.

Once his eyes adjusted to the light Mokuba saw the 3 Pokémon that brought him here.

"Zorua, Shaymin, Victini what are you doing here." Mokuba asked wondering what was happening.

"We are here to tell you your friends have arrived." said Victini.

"Names?" he says.

"Yugi, Joey, and Seto. I believe." said Zorua.

"My big brother is here?" said Mokuba with his mouth open.

"Stop with the questions." ordered Shaymin."And yes he is here and looking for you. He isn't far but I won't tell you where he is." she continued.

"I knew that was coming." sighed Mokuba.

"Now Eevee how do you like Mokuba?" asked Zorua.

'Wait an evaluation oh Ra.' he thought.

"Eevee, Eevee, Eev."

"Man Mokuba you a better trainer than I thought you would be." said Zorua her tail going back and forth with happiness.

Mokuba let out a sigh.

"Now we have to go so go find your big brother, but watch out danger is arising." Victini said

Before Mokuba could speak bright light came and vanished just as quickly.

"What did Victini mean by that? Well we better get going huh." Eevee jumped on the Mokuba's shoulder and nodded to say yes.

'Not for long your easy pickings boy.' thought a strange figure from behind a tree. The man stepped out and laughed, catching Mokuba's attention. He whirled around to see a strange guy. with a red suit.{Wonder who that could be.}

"Who are you and what do you want?" asked Mokuba who was getting weird vibes off this guy.

"I'm a Team Flare grunt and I suggest you hand over that Eevee of yours."

'A Pokémon theif great.' he thought but said "You'll never get my Eevee."

"Guess we'll have to do this the hard way. Go Poochyena." said the grunt. A Pokémon that looked like a black wolf pup burst out of its pokeball baring its fangs. Mokuba looked over to Eevee and nodded his head in the direction of the opposing Pokémon. Eevee got the message and quickly jumped of his shoulder and across from the Poochyena, also baring it's fangs.

"I'll let you have the first move boy."

"Don't underestimate me. Eevee use swift."

Eevee jumped into the air, spun and then shot stars out of its tail.

Poochyena tried to dodge but got hit by one anyway.

"Poochyena go and use bite."

"Double Team."

Eevee made copies of itself and started running in a circle. Poochyena bit and bit trying to find the right one. Till it collapsed from dizziness.

"Come on get up you worthless Pokémon." yelled the grunt. Mokuba was saddened by this but he had a battle to win.

"Eevee use Covet." Eevee obeyed and hearts started to shoot at Poochyena. "Now use Quick Attack." Light went through Eevee and then Eevee charged at a speed that would certainly break the speed limit at Domino.

Poochyena yelped when the Quick Attack hit full force. Poochyena didn't get back up. Mokuba had won.

"Poochyena I'm sorry you have a guy like that for a trainer." Mokuba looked over at the grunt.

"Next time don't underestimate me." Eevee growled for emphasize.

"We'll get that Eevee. Come Poochyena." The grunt walked of not even looking to see if Poochyena was following, which it wasn't.

"Poochyena you don't like him do you?" Poochyena shook its head. It didn't want to go back to that man. And Mokuba didn't blame it.

Eevee and Mokuba looked at each other before nodding at the same time. "Poochyena how would you like to come with us?" Mokuba asked and exclaimed at the same time.

Poochyena perked it ears up. It headed over to rub against Mokuba's legs.

"I'll take that as a yes." Mokuba reached for a pokeball, enlarged it and held it out to Poochyena.

Poochyena pressed it with his paw and went inside. After a few rocks it clicked, signaling it had been caught.

"Welcome Poochyena you need to rest anyways."

Eevee got back on Mokuba's shoulder and the two headed of with there new friend to find Seto.

* * *

**Blue: Now Mokuba has two Pokémon won his first battle with Team Flare and stayed cute in the process alright.**

**Next: Mokuba gets back with the gang. At least I hope that's how it works out.**


	3. Brotherly reunion

**Blue: Hello people and welcome to chapter 3. I plan on Mokuba finding Seto.**

**Bakanaru: Doesn't Mokuba do the gym battle.**

**Blue: That isn't for another 2 chapters.**

**Mokuba: Who is she?**

**Blue: Oh guys meet Bakanaru my Yami. And she is crazy.**

**Seto: What level?**

**Blue: Bakura's level.**

**Bakura: Alright someone to play pranks with.**

**Ryou: What about me?**

**Bakura: I still love you.*Puts hands over mouth.***

**Blue: God Ryou your good.**

**Bakanaru: I need to see if I can get a Tendershipping one shot out of her.**

**Mokuba: Blue doesn't own Pokémon or Yugioh so don't sue her.**

* * *

Mokuba was walking along the path that led Into Santalune City. He was hoping he might find Seto, after hearing he was here he didn't take much breaks as he did before.

"Eevee." whined Eevee trying to keep up with Mokuba.

"I'm sorry Eevee I just want to see my brother again. Lets go to the Pokémon Center." Mokuba apologized

They soon arrived at the Pokémon Center. Nurse Joy took Eevee to get rested while Mokuba washed up.

"Well I'll look tomorrow Eevee needs a break." He said to himself.

He hit the hay for the night with Eevee curled up next to him.{Cute. Just imagine it. You'll be blind for a week by the cuteness.}

* * *

With Seto, Yugi, and Joey

"Finally we're out of that stupid forest and into civilization." said Joey.

"I didn't think you knew words like that, mutt." smirked Kaiba.

"Oh can it moneybags." snapped Joey.

"Well it's getting dark. We should head for the Pokémon Center. We'll search for Mokuba in the morning." suggested Yugi, avoiding a fight.

As much as Seto wanted to search for Mokuba it was getting dark. He knew Mokuba wouldn't travel in the dark, so Mokuba was safe. They headed for the Pokémon Center. Got to there separate rooms{Bakanaru: Why would they share a room? Blue: Oh shut up.}and went to bed. Joey was out as soon as his head hit the pillow. They traveled a long time, without much food.

{Bakura: How did he survive?}

Yugi was sleeping like a log, hoping he would wake up in the game shop tomorrow. Seto took a while but exhaustion finally overpowered him. He was hoping Mokuba was alright. Where ever he was.

* * *

With Mokuba

Eevee awoke to a scent that made his senses tingle. It smelled too similar to Mokuba so he decided to check it out. He quietly pried open the door and sneaked out, not wanting to wake up Mokuba.

Mokuba was awoken anyway feeling the weight shift on the bed. He looked and saw Eevee leaving the room. Instead of calling out he decided to follow being how curious he was.

Eevee smelled the scent strongest from one room. Who ever it was was in here and he was going to find out who it is. Eevee pried open the door again and looked inside. Safe so far. He snuck up to the bed like he was hunting.

Mokuba watched from the doorway quiet as a mouse. He was wondering what was going on.

Eevee gracefully launched up to the bed and went to sniff the person in the bed. Stong scents of pine and cinnamon filled his nose. He smelled just like Mokuba. Out of instinct he licked his face not thinking he was going to wake up.

Mokuba watched in horror hoping the guy wouldn't wake up. Unfortunately lady luck was not on his side. The man stirred and sat up blinking his eyes. He looked down at the Pokemon who just woke him up. "What do you want?" Mokuba gasped it's Seto. It's Seto it has the same voice that could stop anybody in its track.

"Seto." Mokuba breathed out not believing Eevee found his brother for him.

Seto raised his head and widened his eyes. There standing in his doorway was his baby brother.

"For once I'm glad Eevee was curious." Mokuba said with a smile.

"Mokuba." Seto said as he got out of bed to give Mokuba a hug.

"I've been searching for you as soon as I got here." Seto said still in the hug.

"Same here but how did you know I was here?"

"Zorua, Shaymin, and Victini."

"Really they told me earlier today you were coming."

"Eevee." said the fox not like being ignored.

"Oh right, Seto this is Eevee. He's been protecting me." Mokuba said so happy he was back with his brother.

Seto looked at the Eevee which was standing next to Mokuba, with a puffed out chest and its head held high.

Seto picked it up aand looked into it's eyes which resulted in another face lick.

Mokuba giggled as Seto thanked Eevee for helping Mokuba.

"I'll admit this..." Seto started grabbing Mokuba's attention. "You have one cute partner." he said. Mokuba gave him the biggest smile happy his Nii-sama approved of his little Pokémon.

"You know Seto, he reminds me of you."

"Oh really?" Seto raised an eyebrow.

"Yea he's protective, loves me, and has a big ego."

Seto suppressed a chuckle. Eevee just glared at its trainer while Mokuba stuck out his tounge.

"You really think I have a big ego?"

"Brother you proved that when you kept trying to beat Yugi."

"Ok ok now you better get some sleep."

"Alright well see you in the morning Nii-sama."

Mokuba and Eevee left for their room while Seto got back to bed. Feeling happier than when Mokuba went missing a week ago. Then he realized something. How was his disappearance affecting Kaiba Corp. Well one problem at a time. It's not like he has his laptop. He finally went into blackness smiling.

* * *

**Blue: Wow I'm happy with how this turned out. I SO wanted to do brotherly fluff. Oh its so cute.**

**Bakanaru: I thought you hated Seto.**

**Blue: I know but my sisters getting to me, also I can't hate him when he's with Mokuba. And the face lick so cute.**

**Seto: What do you mean your sisters getting to you?**

**Blue: It means my sister is a major Kaiba fangirl.**

**Bakura: Are you going to right a Tendershipping oneshot or not?**

**Blue: Well I have to think of a situation. My Puzzleshipping one just popped into my head. Besides there wasn't much Puzzleshipping in it anyway. I'll try but I can't guarantee anything.**

**Ryou: *Sulks***


	4. Poochyena's revenge

**Blue: Hello in this one Mokuba gets with the rest of the gang. And just to clear stuff up. Mokuba is the ONLY one collecting gym badges. Because he understands the place unlike the rest. And well I think Seto couldn't care less about the gyms.**

**Seto: Got that right. Where were you anyway?**

**Blue: Writing chapter 3 of A princesses world turned upside down. Anyway also that team flare grunt from chapter 2 comes back.**

**Mokuba: What does he want?**

**Blue: Your eevee and poochyena once he finds out you have it.**

**Mokuba: Blue DOESN'T own Yugioh.**

* * *

"What?!" exclaimed Yugi and Joey. They just saw Seto walk in with Mokuba who had a fox like Pokémon at his heels.

"Yea um hey guys." Mokuba said sheepishly.

"When did he get here?" asked Joey not quite understanding the situation.

"Last night actually." answered Mokuba.

"Wait how come we didn't notice you?" Yugi asked.

"I was in my room most of the time."

"Ok but how did Kaiba find you?" Joey asked.

"His Eevee found me in all honesty." Seto answered.

"Eevee?" Joey asked.

Eevee than circled Joey trying to figure out whether or not to trust him. Eevee yipped happily and jumped on Joey causing him to stumble back a bit.

"Looks like Eevee likes you." Yugi laughed.

Eevee than turned his attention to Yugi, circling him like he did Joey. Like with Joey Eevee yipped and jumped. Yugi being smaller fell on his butt.

"Eevee deems you worthy." Mokuba said.

"Of what?" Yugi asked getting up.

"Being his friend. Oh and Joey, better prepare. Having Eevee around is like having another Seto. He has a big ego in his small body. Not kidding last night he tried to stare down Seto." Mokuba laughed at the thought.

"Oh great. The difference is that it can't talk. Which is a good thing." Joey complained.

"Hey Seto did you tell him about the real life duel monsters?" Yugi asked.

"Real life duel monsters?!" Mokuba asked confused.

"Yea come on we'll show you." Yugi said leading Mokuba to the battle arena, Joey and Seto in tow.

* * *

"Ok we better use small ones." suggested Yugi.

"I don't know which is smaller Blue-eyes or Alexandrite?" Seto wondered.

"Well than pick one." Joey said.

"Alright come on out Kuriboh." Yugi said. In a flash of light Kuriboh was out on the field looking around.

"Kuriboh?" Mokuba said.

"Blue-eyes lets go." Kaiba said. Blue-eyes showed up with a mighty roar. Both scaring Mokuba and putting him in awe.

"Wow." was all Mokuba could say.

"Leogun time you got out." Joey said. Leogun showed up with its own roar.{If you don't know the card look it up.}

"Man I'm impressed." Mokuba admitted. Eevee was giving each it's own judgment.

Eevee then stopped hearing something it's ears perked high twitching them in different directions.

"Eevee is something wrong?" Mokuba asked.

Eevee didn't respond.

"Eevee?" Mokuba asked again.

Eevee let out a low growl.

"Eevee what going on."

The three duel monsters on the field started growling as well. Blue-eyes was especially loud.

"What's going on." Yugi asked.

"Hahaha so we meet again squirt." a voice said as it approached them.

Mokuba recognized the voice and narrowed his eyes.

"Mokuba?" Seto asked. Mokuba was not one to get angry.

"What do you want?" Mokuba said clearly angry.

"Mokuba what's going on?" Joey asked.

"This guy..." Mokuba said pointing his thumb over to the guy. "Tried to steal my Eevee yesterday before I came to the Pokémon center."

"Yes and I still want it. That and my Poochyena disappeared yesterday too." The grunt said.

"Maybe if you were a good trainer it wouldn't have. Besides I know it has a better life now without you." Mokuba said.

"How do you know?" The grunt asked.

"Because of this." Mokuba said as he threw a pokeball.

Poochyena came out looking at Mokuba, not noticing his former trainer there.

"Poochyena." growled the grunt.

Poochyena turned around, looking at the grunt. Poochyena immediately growled baring it's fangs.

"You stole my Poochyena." The grunt said extremely ticked.

"I didn't steal anything. Poochyena decided to come with me. Besides you don't deserve him. You are sick. You tried to take my Eevee and you accuse me of stealing." Mokuba yelled.

Seto was surprised at his outburst Mokuba was never one to yell let alone at somebody else. Eevee joined Poochyena in the growling. They had actually become good friends.

"How cute just hand over the Pokémon and I'll leave you alone." the grunt demanded.

Seto was about to intervene, but Mokuba held up his hands to stop. "Poochyena how about a little payback." Mokuba said.

Poochyena yipped and went to the battle field.

"Fine I'll battle you. But I won't lose." the grunt said.

"Oh really well I remember you lost to me miserably last time so I think I got this in the bag."

"That's because I was using that weakling Poochyena."

"Poochyena is not a weakling. If anybody is it's you."

"Ra what did you do with the real Mokuba." Joey said.

"He's been here a week. He must have toughened up a bit." Yugi answered.

Seto just watched proud that Mokuba was standing up for himself.

"Go Muk." the grunt yelled. A giant, purple blob came out of the blob ready for an order.

Mokuba grimaced but kept his cool. "Ok Poochyena use crunch."

"Wait when did it learn that move?" The grunt demanded.

"It's amazing what early morning practice can do?" Mokuba said.

~Flashback~

"Ok Poochyena use bite once more." Mokkuba said. He was having Poochyena practice on his aim.

Poochyena dove at the target his fangs darkening. He destroyed it in one shot. Something bite wouldn't have done.

"Wow what was that?" he asked. "Poochyena use bite again." he ordered.

Poochyena fangs darkened again as he launched at another target. Like the other it was destroyed in one shot.

"Of course." he whispered to himself.

"Hey Poochyena congratulations. You just learned crunch." Mokuba praised. Not even twenty-four hours together and they were already making progress.

~end flashback~

Poochyena launched at Muk and successfully land a bite to it's face.

"Muk use poison gas." the grunt demanded.

Gas started to surround Poochyena and it wasn't looking to good.

"Poochyena move out of the way."

Poochyena moved away from the poison gas but was still poisoned anyway.

"Poochyena payback."

Poochyena got a dark aura around him and charged.

Muk screeched in agony and fell to the ground. Well as much as a blob could.

"No Muk." The grunt returned his pokemon.

"This isn't over yet boy." The grunt sneered before retreated.

"Good riddance." Mokuba mumbled as he picked up Poochyena.

"Man Mokuba that was awesome. He got what was coming to him." Joey praised.

Yugi was also complimenting Mokuba.

Mokuba was looking at Seto with a smile. Seto was happy Mokuba had one. He was actually extremely proud. But he'd never admit it with the mutt around.

After Poochyena was healed they went to look around town. Of course they returned their Pokémon first for they were Pokémon that they would probably attract attention.

They agreed that Mokuba would try out the gym leader Viola tomorrow. The others would try, but they don't know their 'Pokémon's' moves.

'Well of to a new tomorrow.' Mokuba thought.

* * *

**Blue: Well there you have it. Sorry it's short but I'm in a hurry. I have other things to update.**

**Mokuba: Read and Review. *Puppy dog eyes of doom***


End file.
